The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes
Year: 2021
Type: preprint
Abstract: Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here, we assembled 26 haplotype-resolved genome assemblies from 13 genetically diverse sheep using PacBio HiFi sequencing. We constructed a graph-based ovine pan-genome and discovered 142,422 biallelic insertions and deletions, 7,028 divergent alleles and 13,419 multiallelic variations. We then used a graph-based approach to genotype the biallelic SVs in 684 individuals from 45 domestic breeds and two wild species. Integration with RNA-seq data allows to identify candidate expression-associated SVs. We demonstrate a direct link of SVs and phenotypes by localizing the putative causative insertion in HOXB13 gene responsible for the long-tail trait and identifying multiple large SVs associated with the fat-tail. Beyond generating a benchmark resource for ovine structural variants, our study highlights that animal genetic research will greatly benefit from using a pan-genome graph rather than a single reference genome.
Authors: Ran Li, Mian Gong, Xinmiao Zhang, Fei Wang, Zhenyu Liu, Lei Zhang, Mengsi Xu, Yunfeng Zhang, Xuelei Dai, Zhuangbiao Zhang, Wenwen Fang, Yuta Yang, Huanhuan Zhang, Weiwei Fu, Chunna Cao, Peng Yang, Zeinab Amiri Ghanatsaman, Niloufar Jafarpour Negari, Hojjat Asadollahpour Nanaei, Xiangpeng Yue, Yuxuan Song, Xianyong Lan, Weidong Deng, Xihong Wang, Ruidong Xiang, Eveline M. Ibeagha-Awemu, Pat (J.S.) Heslop-Harrison, Johannes A. Lenstra, Shangquan Gan, Yu Jiang
Institutions: Northwest A&F University, Xinjiang Academy of Agricultural and Reclamation Science, Agricultural Research & Education Organization, Shahid Bahonar University of Kerman, Ministry of Agriculture and Rural Affairs, Lanzhou University, Yunnan Agricultural University, The University of Melbourne, Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, University of Leicester, Utrecht University
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
OpenAlex ID: W4200190855